I would like to make a RGB color scheme using the circlize
package. First, I try to make a function so that I only have to input the color and sectors, and the function will do the job
Here is the code:
colorpallete <- function(color, x){
draw.sector(get.cell.meta.data("cell.start.degree", sector.index = x),
get.cell.meta.data("cell.end.degree", sector.index = x),
rou1 = get.cell.meta.data("cell.top.radius", track.index = 1),
rou2 = get.cell.meta.data('cell.bottom.radius', track.index = 3),
col = adjustcolor(col = color, alpha.f = 0.2))
draw.sector(get.cell.meta.data("cell.start.degree", sector.index = x),
get.cell.meta.data("cell.end.degree", sector.index = x),
rou1 = get.cell.meta.data("cell.top.radius", track.index = 1),
rou2 = get.cell.meta.data('cell.bottom.radius', track.index = 2),
col = adjustcolor(col = color, alpha.f = 0.2))
draw.sector(get.cell.meta.data("cell.start.degree", sector.index = x),
get.cell.meta.data("cell.end.degree", sector.index = x),
rou1 = get.cell.meta.data("cell.top.radius", track.index = 1),
rou2 = get.cell.meta.data('cell.bottom.radius', track.index = 1),
col = adjustcolor(col = color, alpha.f = 0.2))
}
circos.initialize(sectors, xlim = c(0, 1))
for(i in 1:3) {
circos.track(ylim = c(0, 1))
}
colset = (c('blue', 'cyan', 'green', 'yellow', 'red', 'violet'))
sectors = letters[1:6]
colorpallete(colset, sectors)
When I try to run the code, it returns the following error:
Error: Length of `sector.index` should only be 1.
How can I make the function corresponds to each list, such as when I call the function, only 'blue' and 'a' get called, followed by 'cyan' and 'b', etc.
Thank you very much in advance
Update: I managed to run the function:
colorpallete <- function(sectors, color){
circos.initialize(sectors, xlim = c(0, 1))
for(i in 1:3) {
circos.track(ylim = c(0, 1))
}
for(i in 1:6){
draw.sector(get.cell.meta.data("cell.start.degree", sector.index = sectors[i]),
get.cell.meta.data("cell.end.degree", sector.index = sectors[i]),
rou1 = get.cell.meta.data("cell.top.radius", track.index = 1),
rou2 = get.cell.meta.data('cell.bottom.radius', track.index = 3),
col = adjustcolor(col = color[i], alpha.f = 0.2))
draw.sector(get.cell.meta.data("cell.start.degree", sector.index = sectors[i]),
get.cell.meta.data("cell.end.degree", sector.index = sectors[i]),
rou1 = get.cell.meta.data("cell.top.radius", track.index = 1),
rou2 = get.cell.meta.data('cell.bottom.radius', track.index = 2),
col = adjustcolor(col = color[i], alpha.f = 0.2))
draw.sector(get.cell.meta.data("cell.start.degree", sector.index = sectors[i]),
get.cell.meta.data("cell.end.degree", sector.index = sectors[i]),
rou1 = get.cell.meta.data("cell.top.radius", track.index = 1),
rou2 = get.cell.meta.data('cell.bottom.radius', track.index = 1),
col = adjustcolor(col = color[i], alpha.f = 0.2))
} circos.clear()}
sectors = letters[1:6]
colset = (c('blue', 'cyan', 'green', 'yellow', 'red', 'violet'))
colorpallete(sectors, colset)
To make custom set of sectors and colors (where it doesn't have to be 6)
colorpallete <- function(sectors, color){
if(length(sectors) != length(color)){
print("Error: sectors should have the same length as color")
} else {
circos.initialize(sectors, xlim = c(0, 1))
for(i in 1:3) {
circos.track(ylim = c(0, 1))
}
for(i in 1:length(sectors)){
draw.sector(get.cell.meta.data("cell.start.degree", sector.index = sectors[i]),
get.cell.meta.data("cell.end.degree", sector.index = sectors[i]),
rou1 = get.cell.meta.data("cell.top.radius", track.index = 1),
rou2 = get.cell.meta.data('cell.bottom.radius', track.index = 3),
col = adjustcolor(col = color[i], alpha.f = 0.2))
draw.sector(get.cell.meta.data("cell.start.degree", sector.index = sectors[i]),
get.cell.meta.data("cell.end.degree", sector.index = sectors[i]),
rou1 = get.cell.meta.data("cell.top.radius", track.index = 1),
rou2 = get.cell.meta.data('cell.bottom.radius', track.index = 2),
col = adjustcolor(col = color[i], alpha.f = 0.2))
draw.sector(get.cell.meta.data("cell.start.degree", sector.index = sectors[i]),
get.cell.meta.data("cell.end.degree", sector.index = sectors[i]),
rou1 = get.cell.meta.data("cell.top.radius", track.index = 1),
rou2 = get.cell.meta.data('cell.bottom.radius', track.index = 1),
col = adjustcolor(col = color[i], alpha.f = 0.2))
}
circos.clear()
}}
sectors = letters[1:4]
colset = (c('darkblue', 'blue', 'darkred', 'red'))
colorpallete(sectors, colset)
Of course, sectors
and colset
need to have the same length